Strain identifier
BacDive ID: 4341
Type strain:
Species: Citrobacter youngae
Strain Designation: 460-61
Strain history: CIP <- 1996, P.A.D. Grimont, Inst. Pasteur, Paris, France <- CDC: strain 460-61
NCBI tax ID(s): 133448 (species)
General
@ref: 7065
BacDive-ID: 4341
DSM-Number: 17578
keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, mesophilic, Gram-negative, motile, rod-shaped
description: Citrobacter youngae 460-61 is a facultative anaerobe, mesophilic, Gram-negative bacterium that was isolated from meat scraps.
NCBI tax id
- NCBI tax id: 133448
- Matching level: species
strain history
@ref | history |
---|---|
7065 | <- CIP <- P. A. D. Grimont, Institut Pasteur, Paris <- CDC |
124017 | CIP <- 1996, P.A.D. Grimont, Inst. Pasteur, Paris, France <- CDC: strain 460-61 |
doi: 10.13145/bacdive4341.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Enterobacterales
- family: Enterobacteriaceae
- genus: Citrobacter
- species: Citrobacter youngae
- full scientific name: Citrobacter youngae Brenner et al. 1993
@ref: 7065
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Enterobacteriales, not validated
family: Enterobacteriaceae
genus: Citrobacter
species: Citrobacter youngae
full scientific name: Citrobacter youngae Brenner et al. 1993
strain designation: 460-61
type strain: yes
Morphology
cell morphology
- @ref: 124017
- gram stain: negative
- cell shape: rod-shaped
- motility: yes
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
7065 | TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) | yes | https://mediadive.dsmz.de/medium/535 | Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water |
36441 | MEDIUM 72- for trypto casein soja agar | yes | Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g) | |
124017 | CIP Medium 3 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3 | |
124017 | CIP Medium 72 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
7065 | positive | growth | 30 | mesophilic |
36441 | positive | growth | 30 | mesophilic |
50271 | positive | growth | 37 | mesophilic |
124017 | positive | growth | 5-41 |
Physiology and metabolism
oxygen tolerance
- @ref: 124017
- oxygen tolerance: facultative anaerobe
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
124017 | 29864 | mannitol | + | fermentation |
124017 | 16947 | citrate | + | carbon source |
124017 | 17716 | lactose | - | fermentation |
124017 | 17632 | nitrate | + | reduction |
124017 | 16301 | nitrite | + | reduction |
124017 | 15792 | malonate | - | assimilation |
124017 | 132112 | sodium thiosulfate | + | builds gas from |
124017 | 17234 | glucose | + | degradation |
antibiotic resistance
- @ref: 124017
- metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
- is antibiotic: yes
- is sensitive: no
- is resistant: yes
metabolite production
- @ref: 124017
- Chebi-ID: 35581
- metabolite: indole
- production: no
metabolite tests
@ref | Chebi-ID | metabolite | voges-proskauer-test | methylred-test |
---|---|---|---|---|
124017 | 15688 | acetoin | - | |
124017 | 17234 | glucose | + |
enzymes
@ref | value | activity | ec |
---|---|---|---|
68382 | alpha-fucosidase | - | 3.2.1.51 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68382 | beta-glucosidase | + | 3.2.1.21 |
68382 | alpha-glucosidase | + | 3.2.1.20 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | beta-galactosidase | + | 3.2.1.23 |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | trypsin | + | 3.4.21.4 |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | valine arylamidase | + | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | lipase (C 14) | - | |
68382 | esterase lipase (C 8) | + | |
68382 | esterase (C 4) | + | |
68382 | alkaline phosphatase | + | 3.1.3.1 |
124017 | oxidase | - | |
124017 | beta-galactosidase | + | 3.2.1.23 |
124017 | alcohol dehydrogenase | - | 1.1.1.1 |
124017 | gelatinase | - | |
124017 | catalase | + | 1.11.1.6 |
124017 | lysine decarboxylase | - | 4.1.1.18 |
124017 | ornithine decarboxylase | - | 4.1.1.17 |
124017 | phenylalanine ammonia-lyase | - | 4.3.1.24 |
124017 | tryptophan deaminase | - | |
124017 | urease | - | 3.5.1.5 |
API zym
@ref | Control | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
124017 | - | + | + | + | - | + | + | - | + | - | + | + | - | + | - | + | + | - | - | - |
API biotype100
@ref | GLU | FRU | GAL | TRE | MNE | SBE | MEL | SAC | RAF | MTE | MAL | LAC | LTE | MbGa | MaGa | CEL | GEN | MbGu | ESC | RIB | ARA | XYL | PLE | RHA | FUC | MLZ | DARL | LARL | XLT | DUL | TAG | GLY | INO | MAN | MTL | TUR | SOR | ADO | HBG | LYX | ERY | MDG | 3MDG | SAT | MUC | LTAT | DTAT | MTAT | DMLT | LMLT | CATE | TATE | TTE | CIT | GRT | GAT | 2KG | 5KG | TRY | NAG | GNT | PAC | PAT | pOBE | QAT | GTE | mOBE | BAT | PPAT | CMT | TGE | BET | PCE | ABT | HIN | LAT | CAP | CYT | HIS | SUC | FUM | GRE | GYT | AVT | ETN | TTN | GLN | ITA | 3OBU | APT | GTT | PRO | DALA | LALA | SER | MNT | PROP | TYR | 2KT |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
124017 | + | + | + | + | + | + | - | - | - | + | + | - | - | + | - | - | + | + | - | + | + | + | - | + | + | - | - | - | - | + | - | + | - | + | - | - | + | - | - | + | - | - | - | + | + | - | - | + | + | + | + | - | - | + | + | + | + | + | - | + | + | - | - | - | - | - | - | - | + | + | - | - | - | + | - | + | - | - | - | + | + | - | + | + | - | - | + | - | + | + | + | + | + | + | + | - | + | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
7065 | meat scraps | South Carolina | USA | USA | North America |
50271 | Meat scraps | South Carolina | USA | USA | North America |
124017 | Food, Meat scraps | South Carolina | United States of America | USA | North America |
isolation source categories
- Cat1: #Engineered
- Cat2: #Food production
- Cat3: #Meat
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
7065 | 2 | Risk group (German classification) |
124017 | 1 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Citrobacter freundii 16S ribosomal RNA | M59291 | 1490 | ena | 546 |
7065 | Citrobacter youngae partial 16S rRNA gene, strain CECT 5335 | AJ564736 | 948 | ena | 133448 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Citrobacter youngae CCUG 30791 | GCA_003818115 | contig | ncbi | 133448 |
66792 | Citrobacter youngae strain CCUG 30791 | 133448.7 | wgs | patric | 133448 |
66792 | Citrobacter youngae CCUG 30791 | 2903312461 | draft | img | 133448 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
motile | yes | 89.672 | no |
gram-positive | no | 98.438 | no |
anaerobic | no | 94.569 | no |
halophile | no | 91.789 | no |
spore-forming | no | 94.311 | no |
glucose-util | yes | 94.58 | no |
flagellated | yes | 54.735 | no |
thermophile | no | 99.256 | no |
aerobic | yes | 77.986 | no |
glucose-ferment | yes | 94.43 | no |
External links
@ref: 7065
culture collection no.: CCUG 30791, DSM 17578, ATCC 29935, CDC 460-61, CECT 5335, CIP 105016
straininfo link
- @ref: 73833
- straininfo: 1753
literature
- topic: Phylogeny
- Pubmed-ID: 25687346
- title: Multilocus sequence analysis of the genus Citrobacter and description of Citrobacter pasteurii sp. nov.
- authors: Clermont D, Motreff L, Passet V, Fernandez JC, Bizet C, Brisse S
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.000122
- year: 2015
- mesh: Bacterial Typing Techniques, Citrobacter/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Genes, Bacterial, Molecular Sequence Data, Multilocus Sequence Typing, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA
- topic2: Transcriptome
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
7065 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17578) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-17578 | |||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
36441 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/16988 | ||||
50271 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 30791) | https://www.ccug.se/strain?id=30791 | |||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
68382 | Automatically annotated from API zym | |||||
73833 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID1753.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
124017 | Curators of the CIP | Collection of Institut Pasteur (CIP 105016) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105016 |